Align Probable fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate WP_013402102.1 CALHY_RS00635 class II fructose-bisphosphate aldolase
Query= SwissProt::P13243 (285 letters) >NCBI__GCF_000166355.1:WP_013402102.1 Length = 278 Score = 192 bits (487), Expect = 9e-54 Identities = 110/286 (38%), Positives = 163/286 (56%), Gaps = 16/286 (5%) Query: 3 LVSMTEMLNTAKEKGYAVGQFNLNNLEFTQAILQAAEEEKSPVILGVSEGAGRYMGGFKT 62 LV++ E+L+ K K + VG FN + +F + ++ AAE+ + P+I+GV++ R++ Sbjct: 2 LVNLNEVLSYTKVKKFGVGMFNGLSADFYEGLIDAAEQLRCPIIIGVAD---RFVDRLDF 58 Query: 63 VVAMVKALMEEYKVTVPVAIHLDHGSSFESCAKAIHAGFTSVMIDASHHPFEENVATTAK 122 + + + +VPV +HLDH S ++ +AI AGFTSVM D S PFEEN+ T + Sbjct: 59 EMIAEVMIFLAKRASVPVCVHLDHAKSLKNIMRAIKAGFTSVMFDGSSLPFEENIKRTKE 118 Query: 123 VVELAHFHGVSVEAELGTVGGQEDDVIAEGVIYADPKECQELVERTGIDCLAPALGSVHG 182 +VE+AH GVSVE ELG VG + D Y P E +E ++T +D LA ++G+VHG Sbjct: 119 IVEIAHSVGVSVEGELGVVGRGDFD-FKNPEFYTKPDEAEEFAQKTQVDALAVSIGTVHG 177 Query: 183 PYKGEPNLGFKEMEEIGKSTGLPLVLHGGTGIPTADIKKSISLGTAKINVNTENQISSAK 242 YKGEP L F+ + EI K LVLHGG+G+ D KK I G K+N+ T+ ++ Sbjct: 178 VYKGEPKLDFERLSEIRKRVDCYLVLHGGSGLSDEDFKKCIEYGINKVNIFTDLTLAINA 237 Query: 243 AVRETLAAKPDEYDPRKYLGPA-----REAIKETVIGKMREFGSSN 283 + E + D L PA RE +K+ I K++ FGS N Sbjct: 238 QLPEFIKQTED-------LTPAIFEKIREIVKQEAIKKLKIFGSYN 276 Lambda K H 0.313 0.131 0.367 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 211 Number of extensions: 7 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 285 Length of database: 278 Length adjustment: 26 Effective length of query: 259 Effective length of database: 252 Effective search space: 65268 Effective search space used: 65268 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory